4898794edd81be5285ea6e544acbedeaeb31bf78
max
  Tue Nov 23 08:10:57 2021 -0800
Fixing pointers to README file for license in all source code files. refs #27614

diff --git src/hg/orthoMap/orthoEval.c src/hg/orthoMap/orthoEval.c
index 7bd9d57..0c1a94a 100644
--- src/hg/orthoMap/orthoEval.c
+++ src/hg/orthoMap/orthoEval.c
@@ -1,94 +1,94 @@
 /* Copyright (C) 2011 The Regents of the University of California 
- * See README in this or parent directory for licensing information. */
+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "orthoEval.h"
 #include "borf.h"
 #include "bed.h"
 #include "altGraphX.h"
 
 
 void orthoEvalTabOut(struct orthoEval *ev, FILE *f)
 /* Tab out an orthoEval record. Skipping the agxBed, and agx records. */
 {
 int i=0;
 assert(ev);
 assert(ev->orthoBedName);
 assert(ev->borf);
 assert(ev->agxBedName);
 fprintf(f, "%s\t", ev->orthoBedName);
 bedCommaOutN(ev->orthoBed, 12, f);
 fprintf(f, "\t");
 borfCommaOut(ev->borf, f);
 fprintf(f, "\t");
 fprintf(f, "%d\t", ev->basesOverlap);
 fprintf(f, "%s\t", ev->agxBedName);
 fprintf(f, "%d\t", ev->numIntrons);
 for(i=0; i<ev->numIntrons; i++)
     fprintf(f, "%d,", ev->inCodInt[i]);
 fprintf(f, "\t");
 for(i=0; i<ev->numIntrons; i++)
     fprintf(f, "%d,", ev->orientation[i]);
 fprintf(f, "\t");
 for(i=0; i<ev->numIntrons; i++)
     fprintf(f, "%d,", ev->support[i]);
 fprintf(f, "\t");
 for(i=0; i<ev->numIntrons; i++)
     fprintf(f, "%s,", ev->agxNames[i]);
 fprintf(f, "\n");
 }
 
 struct orthoEval *orthoEvalLoad(char *row[])
 /* Load a row of strings to an orthoEval. */
 {
 struct orthoEval *oe = NULL;
 int sizeOne = 0;
 AllocVar(oe);
 oe->orthoBedName = cloneString(row[0]);
 oe->orthoBed = bedCommaInN(&row[1], NULL, 12);
 oe->borf = borfCommaIn(&row[2], NULL);
 oe->basesOverlap = sqlUnsigned(row[3]);
 oe->agxBedName = cloneString(row[4]);
 oe->numIntrons = sqlUnsigned(row[5]);
 sqlSignedDynamicArray(row[6], &oe->inCodInt, &sizeOne);
 assert(sizeOne == oe->numIntrons);
 sqlSignedDynamicArray(row[7], &oe->orientation, &sizeOne);
 assert(sizeOne == oe->numIntrons);
 sqlSignedDynamicArray(row[8], &oe->support, &sizeOne);
 assert(sizeOne == oe->numIntrons);
 sqlStringDynamicArray(row[9], &oe->agxNames, &sizeOne);
 assert(sizeOne == oe->numIntrons);
 return oe;
 }
 
 void orthoEvalFree(struct orthoEval **pEv)
 {
 struct orthoEval *ev = *pEv;
 borfFree(&ev->borf);
 freez(&ev->inCodInt);
 freez(&ev->orientation);
 freez(&ev->support);
 freez(&ev->agxNames);
 altGraphXFree(&ev->agx);
 bedFree(&ev->agxBed);
 freez(&ev);
 *pEv = NULL;
 }
 
 struct orthoEval *orthoEvalLoadAll(char *fileName) 
 /* Load all orthoEval from a whitespace-separated file.
  * Dispose of this with orthoEvalFreeList(). */
 {
 struct orthoEval *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[10];
 
 while (lineFileRow(lf, row))
     {
     el = orthoEvalLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }